Julien Lagarde

Systematic cross-study assessment of RNA-Seq experimental workflows for plasma cell-free transcriptome profiling

The paper evaluates RNA-Seq workflows for plasma cell-free transcriptome profiling, finding that technical factors dominate variability over biological differences.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

The paper introduces CapTrap-seq, a method for full-length RNA transcript sequencing, and shows it produces highly accurate transcript models in human tissues.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

RATTLE reconstructs and quantifies transcripts from Nanopore sequencing without a reference genome, showing accuracy and scalability across simulated and experimental data.

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

The paper reanalyzes the CHESS database's new protein-coding predictions and finds most are false positives due to homology errors and lack of experimental evidence.

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing

The paper introduces RNA Capture Long Seq (CLS) to annotate full-length lncRNAs with high throughput and accuracy, doubling annotated complexity compared to short-read methods.

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

The paper analyzes RNA-seq data from multiple mouse tissues to identify genes with conserved expression patterns across species and cell types, revealing evolutionary constraints in gene expression.